{"action":"created","issue":{"url":"https://api.github.com/repos/joey711/phyloseq/issues/332","repository_url":"https://api.github.com/repos/joey711/phyloseq","labels_url":"https://api.github.com/repos/joey711/phyloseq/issues/332/labels{/name}","comments_url":"https://api.github.com/repos/joey711/phyloseq/issues/332/comments","events_url":"https://api.github.com/repos/joey711/phyloseq/issues/332/events","html_url":"https://github.com/joey711/phyloseq/issues/332","id":32198107,"number":332,"title":"subset_taxa by OTU id","user":{"login":"audy","id":115904,"avatar_url":"https://avatars1.githubusercontent.com/u/115904?v=4","gravatar_id":"","url":"https://api.github.com/users/audy","html_url":"https://github.com/audy","followers_url":"https://api.github.com/users/audy/followers","following_url":"https://api.github.com/users/audy/following{/other_user}","gists_url":"https://api.github.com/users/audy/gists{/gist_id}","starred_url":"https://api.github.com/users/audy/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/audy/subscriptions","organizations_url":"https://api.github.com/users/audy/orgs","repos_url":"https://api.github.com/users/audy/repos","events_url":"https://api.github.com/users/audy/events{/privacy}","received_events_url":"https://api.github.com/users/audy/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2014-04-25T00:30:40Z","updated_at":"2017-09-06T04:31:59Z","closed_at":"2014-04-25T02:39:43Z","author_association":"CONTRIBUTOR","body":"Is it possible to use subset_taxa using the taxonomy ID in the tax_table?\n\nBased on what I see here in the code for [`subset_taxa`](https://github.com/joey711/phyloseq/blob/master/R/taxonomyTable-class.R#L109-L125) I don't think it is but I remember seeing a warning about using `OTU` as a column header in the taxonomy table being a no-no.\n\nSo I was thinking this might be planned for the future.\n\nIt could be made possible by adding `rownames(tax_table(phy))` as a column in the taxonomy table but I don't know if that might break `tax_glom` and friends.\n\nAnyway, It would be useful :smile:\n"},"comment":{"url":"https://api.github.com/repos/joey711/phyloseq/issues/comments/327371599","html_url":"https://github.com/joey711/phyloseq/issues/332#issuecomment-327371599","issue_url":"https://api.github.com/repos/joey711/phyloseq/issues/332","id":327371599,"user":{"login":"glickmac","id":7198938,"avatar_url":"https://avatars0.githubusercontent.com/u/7198938?v=4","gravatar_id":"","url":"https://api.github.com/users/glickmac","html_url":"https://github.com/glickmac","followers_url":"https://api.github.com/users/glickmac/followers","following_url":"https://api.github.com/users/glickmac/following{/other_user}","gists_url":"https://api.github.com/users/glickmac/gists{/gist_id}","starred_url":"https://api.github.com/users/glickmac/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/glickmac/subscriptions","organizations_url":"https://api.github.com/users/glickmac/orgs","repos_url":"https://api.github.com/users/glickmac/repos","events_url":"https://api.github.com/users/glickmac/events{/privacy}","received_events_url":"https://api.github.com/users/glickmac/received_events","type":"User","site_admin":false},"created_at":"2017-09-06T04:31:59Z","updated_at":"2017-09-06T04:31:59Z","author_association":"NONE","body":"b1 = tax_glom(ps, taxrank = \"Genus\")\r\nGenus10 = names(sort(taxa_sums(b1), TRUE)[1:10])\r\nx1 = prune_taxa(Genus10, b1)\r\ntax = as.data.frame(x1@tax_table)\r\ntop_ten = as.character(tax$Genus)"}}
{"actor":{"display_login":"glickmac"}}